Many, but not all, input structure files include protein secondary structure
information. In PDB format, secondary structure assignments are described in
HELIX and SHEET records.
When a peptide or protein structure file
that does not include secondary structure assignments is read,
ksdssp is automatically
invoked to generate helix and sheet information.
Ksdssp is also called automatically when
MatchMaker is used with the
Compute secondary structure assignments option,
regardless of whether secondary structure assignments already exist.

In Chimera, helix and sheet assignments are stored as true/false settings
(for each amino acid residue)
of the residue attributesisHelix and isStrand (isSheet).
The assignments are used for drawing protein
ribbons
and may be used by
MatchMaker, depending on its settings.

Parameter settings used are reported
in the Reply Log.
Defaults to be used when ksdssp is called automatically can be changed
with the compute SS dialog
(opened from the Model Panel).
Defaults for the ksdsspcommand, however, cannot be changed
and are given below.
Different values can be specified with the command-line
options.

Ksdssp uses the coordinates of the backbone atoms
(N, CA, C, O, and optionally H) of a protein to determine
which residues are in helices and beta strands. If an amide
hydrogen is missing, it is placed 1.01 Å from N along the bisector
of (1) the vector opposite the bisector of C-N-CA, and (2) the vector
opposite the C-O vector from the previous amino acid.

The calculation is applied to the models containing
atom-spec,
and a blank atom-spec
is interpreted as “all.”
Models that do not appear to contain amino acids
(that is, nonpeptide molecules and nonmolecular objects) are ignored.

Known problem: reassigning secondary structure sets the
ribbon
scaling of some residues to Chimera default; any other scalings
previously in effect need to be reapplied (for example, with
ribscale).

-ccutoffKsdssp estimates the energy of each candidate
hydrogen-bonding interaction and classifies it as a hydrogen bond
if the energy is no greater than (at least as favorable as)
cutoff. The default is –0.5 kcal/mol, as recommended
by Kabsch and Sander, who add that “A good H-bond has about -3
kcal/mol binding energy.”

-hhelix_minHelices must be at least
helix_min residues long; the default is 3.

-sstrand_minBeta strands must be at least
strand_min residues long; the default is 3.
Reducing strand_min to 1 is not recommended,
as there are bridges in many structures that confuse the
algorithm for defining sheets.

-vVerbose mode; send information to the
Reply Log, including helix
and strand residue ranges and whether interstrand relationships are
parallel or antiparallel.

In most cases, the default parameter values
are reasonable for computing secondary structure.